The problem is not that Luke would come of his own will, but more that he was a dangerous person. A Jedi even which made him even more dangerous.
As a Jedi Luke could do quite some damage with mere hand movements and that even fast enough for Vader reacting too late if not prepared for that. With handcuffs Jedi were and are quite hampered there. Most often being restricted to mind tricks and not able to throw the Emperor out of the window of the throne room (as an example there....not that it would have worked any way, but he could have tried).
Furthermore armed imperials could have been alarmed if they knew how Luke looked. Even if in the presence of Vader some of them could have reacted and tried to shoot the rebel at sight....which would have wasted a few possibly good imperials (not that the Emperor would have minded if they weren't useful, but still a waste).
So all in all the handcuffs put the nonsith at ease and at the same time reduced the danger that Luke posed (in case he was not there just for his father and was there to do some damage instead).